Contacts of the strand formed by residues 370 - 375 (chain A) in PDB entry 5WWZ
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with VAL 370 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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330A GLN* 3.6 45.5 - - + +
331A VAL 3.6 6.3 - - - +
332A ARG* 4.1 24.5 - - + +
361A VAL 4.4 1.0 - - - +
363A PRO* 3.4 22.9 - - - +
368A GLU* 2.7 39.4 + - + +
369A PRO* 1.3 77.6 - - - +
371A PHE* 1.3 66.2 + - - +
372A GLU* 4.0 7.9 + - + +
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Residues in contact with PHE 371 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329A VAL 3.6 0.9 - - - +
330A GLN* 3.3 4.5 - - - -
331A VAL* 2.7 50.6 + - + +
333A VAL* 4.0 25.4 - - + -
338A VAL* 4.2 15.5 - - + -
341A VAL* 3.7 32.1 - - + -
342A VAL* 4.2 6.5 - - + -
349A ILE* 4.2 7.6 - - + -
360A ILE* 4.0 17.3 - - + -
361A VAL 3.7 9.9 - - - +
362A THR* 3.7 16.6 - - + -
363A PRO* 3.6 27.1 - - + -
369A PRO 5.1 0.4 - - - -
370A VAL* 1.3 74.9 - - - +
372A GLU* 1.3 60.6 + - - +
373A VAL* 3.9 1.6 + - + -
387A ILE* 4.1 24.0 - - + -
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Residues in contact with GLU 372 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328A THR* 4.4 17.6 - - + +
329A VAL 3.4 6.1 - - - +
330A GLN* 4.4 24.2 - - + +
359A TYR* 3.5 3.1 - - - +
360A ILE* 3.3 3.3 - - - -
361A VAL* 2.9 49.9 + - + +
370A VAL* 4.8 7.6 - - + +
371A PHE* 1.3 74.9 - - - +
373A VAL* 1.3 60.6 + - - +
374A THR* 4.7 1.8 + - - +
314C HIS 5.4 5.4 + - - -
318C HIS* 6.0 2.5 - - + -
319C MET* 4.1 28.4 + - - +
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Residues in contact with VAL 373 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327A THR 3.5 1.6 - - - +
328A THR* 3.2 4.2 - - - -
329A VAL* 3.0 31.3 + - + +
331A VAL* 4.0 24.0 - - + -
358A THR* 3.8 16.8 - - - -
359A TYR 3.5 2.7 - - - -
360A ILE* 3.8 22.7 - - + -
371A PHE 4.6 1.6 - - - +
372A GLU* 1.3 73.6 - - - +
374A THR* 1.3 61.5 + - - +
380A VAL* 4.0 23.9 - - + +
383A ALA* 3.6 27.6 - - + -
384A ARG 5.2 0.9 - - - +
387A ILE* 4.1 11.4 - - + -
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Residues in contact with THR 374 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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322A ASN* 3.5 27.8 - - - +
326A GLN* 4.0 5.6 - - + +
327A THR 3.2 6.3 - - - +
328A THR* 3.0 21.7 + - - +
358A THR* 3.4 4.3 - - - -
359A TYR* 2.7 56.3 + - + -
372A GLU* 4.7 2.1 + - - +
373A VAL* 1.3 75.5 - - - +
375A GLY* 1.3 62.1 + - - +
380A VAL* 3.8 3.4 - - - -
389B MET* 3.4 15.4 - - + +
318C HIS* 3.4 20.8 - - + +
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Residues in contact with GLY 375 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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326A GLN* 4.0 9.9 - - - -
327A THR 2.9 27.8 + - - -
357A HIS 4.8 4.0 - - - -
358A THR* 4.6 5.6 - - - -
374A THR* 1.3 78.3 - - - +
376A MET* 1.3 68.9 + - - +
377A PRO 3.6 0.2 - - - -
380A VAL* 3.4 8.3 - - - +
389B MET* 3.6 16.8 - - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il